def get_factor_info(self, curs, factor_table):
"""
01-31-06
one typical external_database_links looks like:
{"TRANSPATH: MO000024633","EMBL: X12549; DMASCT3","SWISSPROT: P09774; AST3_DROME","PIR: S01165; S01165","FLYBASE: FBgn0002561; l(1)sc"}
only focus on EMBL or SWISSPROT
"""
sys.stderr.write("Getting factor info...")
curs.execute(
"select tf_acc, organism, external_database_links from %s \
where external_database_links is not null" % factor_table)
rows = curs.fetchall()
acc_tax_id2tf_acc = {}
organism2tax_id = {}
for row in rows:
tf_acc, organism, external_database_links = row
if organism in organism2tax_id:
tax_id = organism2tax_id[organism]
else:
tax_id = get_tax_id_from_org(curs, organism)
organism2tax_id[organism] = tax_id
if tax_id: #not some weird name that don't have tax_id
external_database_links = external_database_links[2:-2].split(
'","')
for external_database_link in external_database_links:
xdb_name_acc_ls = external_database_link.split(':')
xdb_name = xdb_name_acc_ls[0]
if xdb_name == 'EMBL' or xdb_name == 'SWISSPROT':
xdb_acc = xdb_name_acc_ls[1]
xdb_acc = xdb_acc.split(';')[0].strip()
key = (xdb_acc.upper(), tax_id)
acc_tax_id2tf_acc[key] = tf_acc
sys.stderr.write("Done.\n")
return acc_tax_id2tf_acc
def get_factor_info(self, curs, factor_table):
"""
01-31-06
one typical external_database_links looks like:
{"TRANSPATH: MO000024633","EMBL: X12549; DMASCT3","SWISSPROT: P09774; AST3_DROME","PIR: S01165; S01165","FLYBASE: FBgn0002561; l(1)sc"}
only focus on EMBL or SWISSPROT
"""
sys.stderr.write("Getting factor info...")
curs.execute("select tf_acc, organism, external_database_links from %s \
where external_database_links is not null"%factor_table)
rows = curs.fetchall()
acc_tax_id2tf_acc = {}
organism2tax_id = {}
for row in rows:
tf_acc, organism, external_database_links = row
if organism in organism2tax_id:
tax_id = organism2tax_id[organism]
else:
tax_id = get_tax_id_from_org(curs, organism)
organism2tax_id[organism] = tax_id
if tax_id: #not some weird name that don't have tax_id
external_database_links = external_database_links[2:-2].split('","')
for external_database_link in external_database_links:
xdb_name_acc_ls = external_database_link.split(':')
xdb_name = xdb_name_acc_ls[0]
if xdb_name=='EMBL' or xdb_name=='SWISSPROT':
xdb_acc = xdb_name_acc_ls[1]
xdb_acc = xdb_acc.split(';')[0].strip()
key = (xdb_acc.upper(), tax_id)
acc_tax_id2tf_acc[key] = tf_acc
sys.stderr.write("Done.\n")
return acc_tax_id2tf_acc
def run(self):
"""
02-01-06
"""
(conn, curs) = db_connect(self.hostname, self.dbname)
tax_id = get_tax_id_from_org(curs, self.organism)
mt_id2no = get_mt_id2no(curs, self.matrix_table)
prom_id2gene_id = self.get_prom_id2gene_id(curs, self.prom_seq_table, self.organism)
self.parse_input_fname(curs, self.input_fname, self.p_value_cut_off, prom_id2gene_id, mt_id2no, tax_id, self.output_table)
if self.commit:
curs.execute("end")
def run(self):
"""
02-01-06
"""
(conn, curs) = db_connect(self.hostname, self.dbname)
tax_id = get_tax_id_from_org(curs, self.organism)
mt_id2no = get_mt_id2no(curs, self.matrix_table)
prom_id2gene_id = self.get_prom_id2gene_id(curs, self.prom_seq_table,
self.organism)
self.parse_input_fname(curs, self.input_fname, self.p_value_cut_off,
prom_id2gene_id, mt_id2no, tax_id,
self.output_table)
if self.commit:
curs.execute("end")
